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- PDB-1aol: FRIEND MURINE LEUKEMIA VIRUS RECEPTOR-BINDING DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1aol
TitleFRIEND MURINE LEUKEMIA VIRUS RECEPTOR-BINDING DOMAIN
ComponentsGP70
KeywordsVIRAL PROTEIN / COAT PROTEIN / VIRAL GLYCOPROTEIN / RETROVIRUS / Viral protein
Function / homologyTLV/ENV coat polyprotein / F-MuLV receptor-binding / ENV polyprotein (coat polyprotein) / suppression by virus of host antigen processing and presentation / suppression by virus of host adaptive immune response / fusion of virus membrane with host plasma membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane ...TLV/ENV coat polyprotein / F-MuLV receptor-binding / ENV polyprotein (coat polyprotein) / suppression by virus of host antigen processing and presentation / suppression by virus of host adaptive immune response / fusion of virus membrane with host plasma membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / integral component of membrane / metal ion binding / Envelope glycoprotein
Function and homology information
Specimen sourceFriend murine leukemia virus
MethodX-RAY DIFFRACTION / MIR / 2 Å resolution
AuthorsFass, D. / Davey, R.A. / Hamson, C.A. / Kim, P.S. / Cunningham, J.M. / Berger, J.M.
CitationJournal: Science / Year: 1997
Title: Structure of a murine leukemia virus receptor-binding glycoprotein at 2.0 angstrom resolution.
Authors: Fass, D. / Davey, R.A. / Hamson, C.A. / Kim, P.S. / Cunningham, J.M. / Berger, J.M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 8, 1997 / Release: Oct 15, 1997
RevisionDateData content typeGroupProviderType
1.0Oct 15, 1997Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GP70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0366
Polyers25,3971
Non-polymers6395
Water3,441191
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)55.300, 68.400, 80.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

#1: Protein/peptide GP70 / SU


Mass: 25397.357 Da / Num. of mol.: 1 / Fragment: RECEPTOR-BINDING DOMAIN / Source: (gene. exp.) Friend murine leukemia virus / Genus: Gammaretrovirus / Species: Murine leukemia virus / Cell line: HIGH FIVE BTI-TN-5B1-4 / Variant: MOLECULAR CLONE 57 / Plasmid name: PVL1393-FRRBD / Genus (production host): Trichoplusia / Cell line (production host): HIGH FIVE, BTI-TN-5B1-4 / Cellular location (production host): SECRETED / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03390
#2: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 2 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Formula: Zn / Zinc
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.99 / Density percent sol: 52 %
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 150 MM ZINC ACETATE, 100 MM SODIUM CACODYLATE, PH 6.5, 19% PEG 8000
Crystal grow
*PLUS
Temp: 20 ℃ / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
1150 mMcalcium acetate1reservoir
2100 mMsodium cacodylate1reservoir
319 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Details: MIRRORS / Detector: IMAGE PLATE / Collection date: Oct 1, 1996
RadiationMonochromator: NI FILTER / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 2 Å / D resolution low: 2 Å / Number obs: 20321 / Observed criterion sigma I: 1.5 / Rsym value: 0.067 / NetI over sigmaI: 11 / Redundancy: 2.5 % / Percent possible obs: 97.2
Reflection shellHighest resolution: 2 Å / Lowest resolution: 2.07 Å / MeanI over sigI obs: 6 / Rsym value: 0.198 / Redundancy: 2.1 % / Percent possible all: 93.9
Reflection
*PLUS
Rmerge I obs: 0.067

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefineMethod to determine structure: MIR / R Free selection details: RANDOM / Cross valid method: THROUGHOUT
Least-squares processR factor R free: 0.264 / R factor R work: 0.223 / R factor obs: 0.223 / Highest resolution: 2 Å / Lowest resolution: 2 Å / Number reflection obs: 20321 / Percent reflection R free: 6.9
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 1785 / Nucleic acid: 0 / Ligand: 31 / Solvent: 191 / Total: 2007
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.90
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS shellHighest resolution: 2 Å / R factor R free: 0.323 / R factor R work: 0.283 / Lowest resolution: 2.09 Å / Number reflection R work: 2290 / Total number of bins used: 8 / Percent reflection R free: 6.8

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